贵州喀斯特地区碳酸盐岩表生古菌群落结构及多样性研究——以南江大峡谷为例

唐 源; 连 宾; 程建中

doi:10.11932/karst20170206

贵州喀斯特地区碳酸盐岩表生古菌群落结构及多样性研究——以南江大峡谷为例

doi: 10.11932/karst20170206

1.
中国科学院地球化学研究所环境地球化学国家重点实验室
2.
南京师范大学生命科学学院

基金项目: 国家自然科学基金项目（41503080）；贵州省科学技术基金项目（黔科合J字 [2014]2168号）；贵州省科技支撑计划项目农业攻关（黔科合NY[2015]3001-1；NY[2013]3019）；贵州省科技重大专项计划（黔科合重大专项字[2014]6015-2-1）；中国科学院地球化学研究所领域前沿项目

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出版历程
- 发布日期: 2017-04-25

Archaeal community structure and diversity of the carbonate rocks in karst regions, Guizhou：A case study of the Nanjiang canyon

1.
State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences
2.
School of Life Science, Nanjing Normal University

摘要

摘要: 为了研究贵州喀斯特地区碳酸盐岩表生古菌群落结构的多样性，应用16S rDNA文库技术，对采集于贵州南江大峡谷的白云岩和石灰岩样品进行基因文库的构建和限制性片段长度多态性(RFLP)分析。用限制性核酸内切酶MspⅠ对两个文库中分别随机挑选的300个阳性克隆子进行酶切分型，白云岩和石灰岩16S rDNA基因文库各得到14和13个基因型，其覆盖率分别为95.4%和91.3%，香农指数分别为2.14和1.93。系统发育分析表明白云岩和石灰岩表生古菌克隆子全部归属于泉古菌门（Crenarchaeota），代表性克隆与GenBank数据库已有16S rRNA序列的相似性为96%～100%，且最高相似性序列均来源于土壤及岩石环境的未可培养古菌序列。
- 白云岩 /
- 石灰岩 /
- 古菌 /
- 多样性 /
- 喀斯特
Abstract: Guizhou is one of the three largest karst regions in the world where vast expanses of karst develop well. The carbonate rock area is 13×104 km2, covering 73% of total land surface area of the province. Carbonate rock is very challenging for organisms to live in it owing to its features, such as arid environment, nutritional deficiency, and great temperature fluctuations. However, there are various microorganisms on its surface and in its cracks, which play a crucial role in biogeochemical cycle. The Nanjiang canyon is a typical karst canyon, which is praised as "Karst Ecosystem Museum". It is located in Kaiyang County of Guizhou Province, southwestern China. And there are a lot of exposed carbonate rocks in this area. In order to study the archaeal diversity of carbonate rocks in Guizhou karst areas, we investigated the archaeal community structure in dolomite and limestone rocks from Nanjiang canyon using 16S rDNA gene clone libraries combined with Restriction Fragment Length Polymorphism (RFLP) analysis. Genomic DNA of rock samples were collected using the UltraCleanTMSoil DNA Isolation Kit. PCR amplification of the archaeal 16S rRNA gene was performed using universal primers 27F and 958R. The PCR products were ligated into the pGEM-T Easy Vector SystemⅠand transformed into competent E.coli JM109 cells and then constructed the dolomite and limestone clone libraries. Randomly selected 300 positive clones from each clone library were identified by RFLP with restriction endonuclease Msp I. In total, 14 and 13 genotypes were obtained from dolomite and limestone clone libraries, respectively. The rarefaction curves indicate that the major part of the diversity in the clone libraries was covered. The coverage C values of dolomite and limestone clone libraries are 95.4% and 91.3%, and Shannon-Wiener indexes are 2.14 and 1.93, respectively. The diversity of indexes shows that the diversity of archaea is much lower than the bacterial and fungal diversity, and the archaeal diversity of dolomite is slightly higher than that of limestone. The phylogenetic analysis reveals that all clones from the two clone libraries are affiliated to the phylum Crenarchaeota. The similarities between the representative clone sequences from carbonate rocks and their closest sequences deposited in GenBank range from 96% to 100% and all of the matches are from uncultured archaeal clones. Meanwhile, most of the archaeal sequences are closely related to environmental clones from soil and rock environments.
- dolomite /
- limestone /
- archaea /
- diversity /
- karst

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参考文献(46)

[1]	连宾. 碳酸盐岩风化成土过程中的微生物作用［J］. 矿物岩石地球化学通报, 2010, 29(1): 52-56.
[2]	张天汉，代玉，王智慧，等. 贵州关岭县喀斯特峰丛石漠区苔藓群落生态特征［J］. 中国岩溶, 2014, 33(2): 192-200.
[3]	Gorbushina A A. Life on the rocks ［J］. Environmental Microbiology, 2007, 9(7): 1613-1631.
[4]	Hose L D, Palmer A N, Palmer M V, et al. Microbiology and geochemistry in a hydrogen-sulphide-rich karst environment ［J］. Chemical Geology,2000,169(3/4):399-423.
[5]	Horath T, Bachofen R. Molecular Characterization of an Endolithic Microbial Community in Dolomite Rock in the Central Alps (Switzerland) ［J］. Microbial Ecology, 2009, 58(2): 290-306.
[6]	Wong F K Y, Lau M C Y, Lacap D C, et al. Endolithic Microbial Colonization of Limestone in a High-altitude Arid Environment ［J］. Microbial Ecology, 2010, 59(4): 689-699.
[7]	Tang Y, Lian B. Diversity of endolithic fungal communities in dolomite and limestone rocks from Nanjiang Canyon in Guizhou karst area, China ［J］. Canadian Journal of Microbiology, 2012, 58(6): 685-693.
[8]	Tang Y, Lian B, Dong H L, et al. Endolithic bacterial communities in dolomite and limestone rocks from the Nanjiang Canyon in Guizhou karst area (China) ［J］. Geomicrobiology Journal, 2012, 29(3): 213-225.
[9]	Takai K, Moser D P, DeFlaun M, et al. Archaeal diversity in waters from deep South African gold mines ［J］. Applied and Environmental Microbiology, 2001, 67(12): 5750-5760.
[10]	姜丽晶, 彭晓彤, 周怀阳, 等. 非培养手段分析珠江口淇澳岛海岸带沉积物中的古菌多样性［J］. 海洋学报, 2008, 30(4): 114-122.
[11]	李曙光, 皮昀丹, Zhang Chuan-lun. 古菌研究及其展望［J］. 中国科学技术大学学报, 2007, 37(8): 830-838.
[12]	Volkl P, Huber R, Drobner E, et al. Pyrobaculum-Aerophilum Sp-Nov, a Novel Nitrate-Reducing Hyperthermophilic Archaeum ［J］.Applied and Environmental Microbiology, 1993, 59(9): 2918-2926.
[13]	Bonnie C, Sandy Y, Ken F. Archaeal habitats-from the extreme to the ordinary ［J］. Canadian Journal of Microbiology, 2006, 52(2): 73-116.
[14]	Schleper C, Jurgens G, Jonuscheit M. Genomic studies of uncultivated archaea ［J］. Nature Reviews Microbiology, 2005, 3(6): 479-488.
[15]	Galand P E, Lovejoy C, Vincent W F. Remarkably diverse and contrasting archaeal communities in a large arctic river and the coastal Arctic Ocean ［J］. Aquatic Microbial Ecology, 2006, 44(2): 115-126.
[16]	Herndl G J, Reinthaler T, Teira E, et al. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean ［J］. Applied and Environmental Microbiology, 2005, 71(5): 2303-2309.
[17]	Walsh D A, Papke R T, Doolittle W F. Archaeal diversity along a soil salinity gradient prone to disturbance ［J］. Environmental Microbiology, 2005, 7(10): 1655-1666.
[18]	Yan B, Hong K,Yu Z N. Archaeal communities in mangrove soil characterized by 16S rRNA gene clones ［J］. Journal of Microbiology, 2006, 44(5): 566-571.
[19]	Beja O, Koonin E V, Aravind L, et al. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces ［J］. Applied and Environmental Microbiology, 2002, 68(1): 335-345.
[20]	Bintrim S B, Donohue T J, Handelsman J, et al. Molecular phylogeny of archaea from soil ［J］. Proceedings of the National Academy of Sciences of the United States of America, 1997, 94(1): 277-282.
[21]	Huber T, Faulkner G, Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments ［J］. Bioinformatics, 2004, 20(14): 2317-2319.
[22]	Cole J R, Chai B, Marsh T L, et al. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy ［J］. Nucleic Acids Research, 2003, 31(1): 442-443.
[23]	Altschul S F, Gish W, Miller W, et al. Basic Local Alignment Search Tool ［J］. Journal of Molecular biology, 1990, 215(3): 403-410.
[24]	Thompson J D, Gibson T J, Plewniak F, et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools ［J］. Nucleic Acids Research, 1997, 25(25): 4876-4882.
[25]	Kimura M. A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide-Sequences ［J］. Journal of Molecular Evolution, 1980, 16(2): 111-120.
[26]	Kumar S, Tamura K, Nei M. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment ［J］. Briefings in Bioinformatics, 2004, 5(2): 150-163.
[27]	Good I J. The Population Frequencies of Species and the Estimation of Population Parameters ［J］. Biometrika, 1953, 40(3/4): 237-264.
[28]	Shuang J L, Zhang X Y, Zhao Z Z, et al. Bacterial phylogenetic diversity in a Spartina marsh in China ［J］. Ecological Engineering, 2009, 35(4): 529-535.
[29]	Hill T C J, Walsh K A, Harris J A, et al. Using ecological diversity measures with bacterial communities ［J］. FEMS Microbial Ecology, 2003, 43(1): 1-11.
[30]	Hansel C M, Fendorf S, Jardine P M, et al. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile ［J］. Applied and Environmental Microbiology, 2008, 74(5): 1620-1633.
[31]	Delong E F. Archaea in Coastal Marine Environments ［J］. Proceedings of the National Academy of Sciences of the United States of America, 1992, 89(12): 5685-5689.
[32]	MacGregor B J, Moser D P, Alm E W, et al. Crenarchaeota in Lake Michigan sediment ［J］. Applied and Environmental Microbiology, 1997, 63(3): 1178-1181.
[33]	Stein L Y, Jones G, Alexander B, et al. Intriguing microbial diversity associated with metal-rich particles from a freshwater reservoir ［J］. Fems Microbiology Ecology, 2002, 42(3):431-440.
[34]	Stein L Y, La Duc M T, Grundl T J, et al. Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments ［J］. Environmental Microbiology, 2001, 3(1): 10-18.
[35]	Buckley D H, Graber J R, Schmidt T M. Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils ［J］. Applied and Environmental Microbiology, 1998, 64(11): 4333-4339.
[36]	Jurgens G, Saano A. Diversity of soil Archaea in boreal forest before, and after clear-cutting and prescribed burning ［J］. Fems Microbiology Ecology, 1999, 29(2): 205-213.
[37]	Ochsenreiter T, Selezi D, Quaiser A, et al. Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR ［J］. Environmental Microbiology, 2003, 5(9): 787-797.
[38]	Lee E Y, Lee H K, Lee Y K, et al. Diversity of symbiotic archaeal communities in marine sponges from Korea ［J］. Biomolecular Engineering, 2003, 20(4/6): 299-304.
[39]	Margot H, Acebal C, Toril E, et al. Consistent association of crenarchaeal Archaea with sponges of the genus Axinella ［J］. Marine Biology, 2002, 140(4): 739-745.
[40]	Dawson S C, DeLong E F, Pace N R. Phylogenetic and ecological perspectives on uncultured Crenarchaeota and Korarchaeota ［C］.// Dworkin M, Falkow S, Rosenberg E, et al. The prokaryotes. New York: Springer, 2006: 281-289.
[41]	Spear J R, Walker J J, McCollom T M, et al. Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem ［J］. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(7):2555-2560.
[42]	Stahl D A, de la Torre JR. Physiology and diversity of ammonia-oxidizing archaea ［J］. Annual Review Microbiology, 2012, 66(4):83-101.
[43]	Leininger S, Urich T, Schloter M, et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils ［J］. Nature, 2006, 442(7104): 806-809.
[44]	Francis C A, Roberts K J, Beman J M, et al. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean ［J］. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(41):14683-14688.
[45]	Lian B, Chen Y, Tang Y. Microbes on carbonate rocks and pedogenesis in karst regions ［J］.Journal of Earth Science, 2010, 21(S1):293-296.
[46]	连宾, 袁道先，刘再华. 岩溶生态系统中微生物对岩溶作用影响的认识［J］. 科学通报, 2011, 56(26): 2158-2161.